Multi-stage sampling together with hierarchical/ mixed effects models: which packages?

Dear R experts,

I sent this question to the r-help list but didn’t get much response, probably because it is more of a stats question. But as this blog is syndicated on r-bloggers I thought I would try it again here on this blog. If I am barking up the wrong tree, feel free to flame.

When I have to analyze educational datasets with samples of children from samples of schools and which include sampling weights, I use the survey package e.g. to calculate means and confidence intervals or to do a linear model. But this kind of design (e.g. children nested inside schools) also as I understand it requires looking at the mixed effects. But this isn’t possible using the survey package. Perhaps I am better advised to use nlme - I guess I could use the sample weights as predictors in nlme regressions but I don’t think that is correct.

It seems that this kind of design (in fact any stratified survey sample which includes nested levels) needs analysing from both perspectives - (survey weights and mixed effects) at once - but the packages of choice for each of these perspectives, survey and nlme, each don’t seem to have slots for the other perspective.

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